Help finding a good primer on the Theory of Evolution.

Is that some what accurate paraphrase of the theory on how DNA (or at least precursors) came to be?

Not really, to be honest. It's also nothing to do with Evolution. Evolution, in its purest form, discusses how DNA (or RNA, or any other genetic material) changes. It doesn't say anything about where that genetic material may have come from.

It may be a genetic algorithm some bored programmer put together. They evolve just like the more widely known living systems and the theory of Evolution describes them.

Is that some what accurate paraphrase of the theory on how DNA (or at least precursors) came to be?

Not really, to be honest. It's also nothing to do with Evolution. Evolution, in its purest form, discusses how DNA (or RNA, or any other genetic material) changes. It doesn't say anything about where that genetic material may have come from.

This strikes me as going a bit too far. I don't think you can draw a clear line between evolution and abiogenesis. How can you exclude some kind of intermediate state where natural selection can act but where there's no genetics?

Think prions. They're a self-catalyzing protein, arguably non-living, and definitely without genetics. In our case they rely on a host organism producing the healthy version of the protein, but what's to rule out something like that being the start of a metabolic cycle in the amino acid soup of early Earth?

Is that some what accurate paraphrase of the theory on how DNA (or at least precursors) came to be?

Not really, to be honest. It's also nothing to do with Evolution. Evolution, in its purest form, discusses how DNA (or RNA, or any other genetic material) changes. It doesn't say anything about where that genetic material may have come from.

This strikes me as going a bit too far. I don't think you can draw a clear line between evolution and abiogenesis. How can you exclude some kind of intermediate state where natural selection can act but where there's no genetics?

Think prions. They're a self-catalyzing protein, arguably non-living, and definitely without genetics. In our case they rely on a host organism producing the healthy version of the protein, but what's to rule out something like that being the start of a metabolic cycle in the amino acid soup of early Earth?

Carpentry is the science (and art) of turning raw wood into useful and/or decorative objects. It doesn't care how it is that trees came to be, nor why wood is well-suited for some projects but particularly ill-suited for others. Carpentry starts with "we have trees" and continues to "what can we do with it?".

Evolution is the study of genetic drift over time. It doesn't care how those genes came to be, nor why certain genes do some things, nor why some coding seems to be particularly circuitous. Evolution starts with "we have genes" and continues with "how do they change over time?".

Evolution is the study of genetic drift over time. It doesn't care how those genes came to be, nor why certain genes do some things, nor why some coding seems to be particularly circuitous. Evolution starts with "we have genes" and continues with "how do they change over time?".

Seems like this begs the question. I don't see why you have to have genes per se, just heritable variation under the influence of natural selection.

Evolution is the study of genetic drift over time. It doesn't care how those genes came to be, nor why certain genes do some things, nor why some coding seems to be particularly circuitous. Evolution starts with "we have genes" and continues with "how do they change over time?".

Seems like this begs the question. I don't see why you have to have genes per se, just heritable variation under the influence of natural selection.

I'll admit I'm using "gene" in the loosest possible sense: that which allows the transmission of heritable variation under the influence of natural selection.

The larger point is, of course, that evolution takes the existence of some mechanism by which one generation tells the next how to build itself (eg. genes) and studies how those instructions change over time. It doesn't concern itself with how the cycle began, just how it continues and changes now that it's going.

Biology, as a larger discipline, is interested in how life began. Evolution, as a "mere" aspect of biology, doesn't.

A better analogy: gravity is the study of how matter attracts matter; it doesn't care where the matter came from, merely how it is attracted to other bits of matter. Physics, the larger discipline, cares where matter came from, but gravity just cares about the attraction of extant matter.

Yes, "study of" should probably have been "set of rules describing and defining"...

Is that some what accurate paraphrase of the theory on how DNA (or at least precursors) came to be?

Not really, to be honest. It's also nothing to do with Evolution. Evolution, in its purest form, discusses how DNA (or RNA, or any other genetic material) changes. It doesn't say anything about where that genetic material may have come from.

This strikes me as going a bit too far. I don't think you can draw a clear line between evolution and abiogenesis. How can you exclude some kind of intermediate state where natural selection can act but where there's no genetics?

Generally speaking, evolutionary biology does not directly address the question of abiogenesis, which is more of a molecular biology question. Evolutionary biology steps in once you have self-replicating information (although as you point out DNA or even RNA may not actually be a requirement although as far as we know at the moment it probably is).

Megalodon wrote:

Think prions. They're a self-catalyzing protein, arguably non-living, and definitely without genetics. In our case they rely on a host organism producing the healthy version of the protein, but what's to rule out something like that being the start of a metabolic cycle in the amino acid soup of early Earth?

Prions are not really subject to natural selection though since the host, and not the prion, decides the composition of the protein. They may be self-replicating (in a sense) but they're not actually evolving.

This strikes me as going a bit too far. I don't think you can draw a clear line between evolution and abiogenesis. How can you exclude some kind of intermediate state where natural selection can act but where there's no genetics?

You can, and you have to. Abiogenesis is nothing to do with natural selection as it has no selective pressure, no inheritance, no genetic material. That only arrived when strings of nucleic acids did, because before them, proteins popped up by chance alone, nothing coded for them or catalysed their production other than other chance proteins (like various ligases, which are known to spontaneously assemble into self-replicating chains).

Quote:

Think prions. They're a self-catalyzing protein, arguably non-living, and definitely without genetics. In our case they rely on a host organism producing the healthy version of the protein, but what's to rule out something like that being the start of a metabolic cycle in the amino acid soup of early Earth?

Prions lack any form of inheritance. They're in the same group as abiogenesis, molecular biology. Prions in particular pre-suppose a functioning living cell (like most viruses, with exceptions), they're meaningless without one, just another conformation of a molecule which can well have thousands of conformations.

The big difference between a prion - which is just a particular conformation (or fold) of a protein - and a virus is that viruses can evolve and can undergo reverse transcription and horizontal gene transfer. Some viruses contain coding for cellular machinery which all cells must have anyway (e.g. mimivirus) and one theory goes that the nucleus of a eukaryote cell is viral in origin.

Prions just fuck shit up without contributing anything. They're the yellowjackets of biology.

As long as it replicates with modifications (and with some autonomy for that process), it is subject to evolution. Evolution doesn't have to use nucleic acids for heredity. Life on other planets may not, and still evolve.

As long as it replicates with modifications (and with some autonomy for that process), it is subject to evolution. Evolution doesn't have to use nucleic acids for heredity. Life on other planets may not, and still evolve.

First post, this page. I stated that it may even be a genetic algorithm!

The OP should read The Greatest Show On Earth by Dawkins. It's *exactly* what he is looking for, and anyone else wanting a first rate introduction to the ToE, that also includes clear refutations of the main lies and propaganda put out by the creationsists.

I can't believe this thread hit page 2 and 49 posts and no-one mentioned this book!

As for whoever asked what would disprove the Theory Of Evolution? I believe JBS Haldane put it best: rabbits in the pre-cambrian

You can, and you have to. Abiogenesis is nothing to do with natural selection as it has no selective pressure, no inheritance, no genetic material.

Say you have a soup of amino acids with some group of proteins that is self-catalyzing. The efficiency is extremely low, but they have an energy gradient from lightning generated chemicals or minerals or whatever, so over time they convert most of the oceans over to their chemistry. Then somewhere another protein shows up that is also self-catalyzing, except it's only self catalyzing in combination with the others, and it has the effect of making one of the reactions the original proteins use more efficient, or maybe it provides a substitute electron donor for one of the reactions they need except powered by sunlight instead of a mineral that's only replenished slowly from steam vents. This new combination of proteins is more efficient so it has a selective advantage, and it has heritability because once that protein enters an area it will quickly make copies of itself and all instances of the old cocktail will thereafter have the new protein added.

This appears to have heritability and selection, even though it's primitive. We might call this pre-genetic heritability. Evolution can act on these proteins.

Now I don't know that that's what happened, but I think it would be an instance of evolution, not just "NOPE, abiogenesis, throw it over the fence and yell at them if they ever try to bring it back". The most interesting aspect of abiogenesis is how we get evolution going, the very first chemistry that natural selection can act on, because you can't say a priori that that's genetics as we know it. Everything after that is relatively easy because evolution is so powerful, but that first cocktail has to occur naturally with some significant probability in the absence of genetics and evolution. When we find that cocktail we will have an answer for abiogenesis even if we don't have proof it's what we used.

^^^^ How are you going to duplicate those proteins and pass their pattern onto that next duplication so it can happen yet another time? That's inheritance. You're just saying you've got it without showing a mechanism. What does "self-catalyzing" mean? How does it work?

^^^^ How are you going to duplicate those proteins and pass their pattern onto that next duplication so it can happen yet another time? That's inheritance. You're just saying you've got it without showing a mechanism. What does "self-catalyzing" mean? How does it work?

Promoting each others formation from existing raw materials. A prion is a trivial case that happens with pre-made proteins. Now imagine this happening with raw amino acids or naturally occurring "proteinoids". This could be very low speed and low efficiency at first without modern life which would come in and gobble everything up.

For example imagine a very small and simple protein forms by chance that is slightly better than chance at promoting one of the precursors for itself. Then with these precursors slightly more plentiful in that area, more instances of that protein happen, and eventually a varient happens that builds in a different way on that precursor, that produces one of the other precursors. And so on. This is natural selection as a matter of definition even though it is not genetic.

The fact that the "proteins first" model of abiogenesis is one of two major hypotheses suggests that others consider this credible.

Anyway, I don't even want to suggest that I think this is what happened. What I want to do is reject this notion that evolution is genetic as a matter of definition. That's begging the question. Anywhere you have heritability, however roundabout, natural selection has traction.

You and Hat are having a "which came first, chicken or egg?" discussion. Your side is lacking in detail, but the overall outline appears sound.

Genetics is about information transfer. The means, nucleic acids, do not define the concept. You're attacking nucleic acid-based genetics, not the more abstract concept. Sticking to discussion of the mechanism avoids the terminology based disputation.

I'm with Hat that current prions rely upon the whole panoply of life. I would like to read from you a more detailed exposition of the bootstrapping of life from prion-like-proteins, or citations thereto.

^^^^ How are you going to duplicate those proteins and pass their pattern onto that next duplication so it can happen yet another time? That's inheritance. You're just saying you've got it without showing a mechanism. What does "self-catalyzing" mean? How does it work?

Promoting each others formation from existing raw materials. A prion is a trivial case that happens with pre-made proteins. Now imagine this happening with raw amino acids or naturally occurring "proteinoids". This could be very low speed and low efficiency at first without modern life which would come in and gobble everything up.

For example imagine a very small and simple protein forms by chance that is slightly better than chance at promoting one of the precursors for itself. Then with these precursors slightly more plentiful in that area, more instances of that protein happen, and eventually a varient happens that builds in a different way on that precursor, that produces one of the other precursors. And so on. This is natural selection as a matter of definition even though it is not genetic.

The fact that the "proteins first" model of abiogenesis is one of two major hypotheses suggests that others consider this credible.

Anyway, I don't even want to suggest that I think this is what happened. What I want to do is reject this notion that evolution is genetic as a matter of definition. That's begging the question. Anywhere you have heritability, however roundabout, natural selection has traction.

I think the forest is being missed for the trees, genetic and heritable doesn't mean nucleic acids, genetic is simply relating to the origination of something, ie the genetic fallacy in logic. Your example seems fine as a system subject to evolutionary action, if proteins were found capable, perhaps some were long ago. But evolution doesn't necessarily have to act on living things, the Speigelman experiment with QBeta phage RNA and replicase for example, when pressures where applied the molecules changed.

I'm asking you to do more homework first and tell us a story, like Hat does every once in while, and how BadAndy could when he wasn't trolling for a fight. Guess I need to heed my own advice too. And TheSpaniard could give us a short precis of the Speigelman experiment with QBeta phage RNA and replicase.

I, too, would be interested in hearing more about plausible "protein first" models, because I find it hard to find the idea plausible, at least not in the way Megalodon seems to be suggesting with proteins being the first genetic material (this is what you are suggesting, right?).

I don't doubt that primitive proteins played a role in the environment where life originated (I'm a big fan of the hydrothermal vent hypothesis, because it neatly solves both the concentration problem and the energy problem). It has been shown experimentally that abiotic peptides can form in such environments (Huber and Wächtershäuser 1998 [PDF]), and this paper by Milner-White and Russell (2008) [PDF] is an interesting look at trying to model what kinds of conformations such early peptides might have taken.

However, I have never seen any models that suggest heredity in such systems and selection acting on such systems, not in the ways you suggest, Megalodon. It seems to me more likely that such proteins were simply part of the environment by chance through "chemical evolution" (which is not the same as biological evolution; it is my understanding that chemical evolution is about changes in chemical content and reactions over time, and not about replication and heredity) of abiotic geochemistry, same as all the other biomolecules that would have been forming over that time. Some may have had catalytic properties and were early enzymes by chance, helping to create other biomolecules. Even then, though, there is nothing like biological evolution happening. RNA ribozymes would have been the same. But, where RNA has the advantage is that ribozymes have been shown to have the potential to catalyze their own self-replication (true RNA only self-replication hasn't happened experimentally yet, and who knows, it may actually need protein helpers of the type that may have been in the environment back then; even if so, there is still no known mechanism of heredity for those proteins yet at that time). And, once one of those self-replicators formed, the evolutionary game would have been afoot.

You can't have biological evolution without heredity. There is a well-known mechanism of heredity through replication of nucleic acid sequences. There is no known mechanism of heredity through replication of amino acid sequences (that I am aware of) without also involving nucleic acid sequences, while there seems to be a strong possibility of nucleic acid sequence heredity without involving proteins, as the evidence suggests that ribozyme self-replication is possible, but we just haven't discovered the right ribozyme (by best estimates, nature had about 300 million years of geochemistry to play with it from the end of late heavy bombardment to the first fossil evidence of life; we've been at it for a couple of decades ).

Now, I don't deny that something like biological evolution could happen in a population of proteins with prions involved (with the evolution being the change in conformation frequencies in the population [originally based on the random formation of different prions, perhaps with selection favoring conformations from prions that could overpower conformations forced by other random prions?], I guess), and I admit the possibility exists that such a system could have been present during abiogenesis and maybe had had an effect on the formation of the first nucleic acid replicators, but I would need to see at least a plausible model showing the possibility and likelihood before I could seriously entertain the possibility. As far as I know, no such models or hypotheses exist yet, but if you know of any, I'd love to read them.

Even with that, I still think it's a stretch to call that the origin of biological evolution on Earth. I mean, you'd really have to show that such prion conformation evolution (remember, only conformations might be considered heredity, since there's no way to influence sequence replication) facilitated the origin of nucleic acid replication, and then those replicators took it from there under what we more easily recognize as biological evolution (more easily because of the clear mechanism of heredity). And, like I said, while the possibility, however small, does exist, I'd really prefer to see a good model and some good evidence to back it up.

At least, that is my understanding. I am definitely not an expert; just an interested amateur High School biology teacher who's stumbled across some papers here and there. I welcome any corrections to any and all of my misunderstandings.

Even with that, I still think it's a stretch to call that the origin of biological evolution on Earth. I mean, you'd really have to show that such prion conformation evolution (remember, only conformations might be considered heredity, since there's no way to influence sequence replication) facilitated the origin of nucleic acid replication, and then those replicators took it from there under what we more easily recognize as biological evolution (more easily because of the clear mechanism of heredity). And, like I said, while the possibility, however small, does exist, I'd really prefer to see a good model and some good evidence to back it up.

My goal is not to make a case for the possibility, but rather object to that possibility being dismissed as an instance of evolution by natural selection as a matter of definition, even if it had happened.

Now it's been pointed out to me that "gene" does not strictly entail "nucleic acids", which was a point that hadn't occurred to me and could have caused confusion in the terminology I've used. In that sense proteins working the way I've described would in some sense be implementing genetic heritability.

But, Hat was specific in pinning evolution to nucleic acids, so my objection to that still stands.

If my idea can be dismissed by the science rather than by the definition, that would be entirely satisfactory for me. Its only purpose was to illustrate the gap I felt Hat's definition did not satisfactorily address.

I'd say with good reason. Biological evolution is the change in gene frequencies in a population of replicators (even using "gene" in the most abstract "unit of inheritance" sense) over time by various mechanisms. On earth, in all life as we know it as yet discovered, genes are made of nucleic acids. They are the material of inheritance and they are essentially the replicators. All evidence suggests that this has always been the case, even in the pre-cellular system of replicators that gave rise to cellular life. For all intents and purposes, biological evolution of modern life on earth began with nucleic acid replicators.

Any claim otherwise is going to need at the very least a very solid model, and even better, experimental support of such a model. Otherwise, you are needlessly multiplying entities, and Occam's razor has some pretty pointed things to say about that.

(Yes, such "what if" scenarios can be interesting to think about and can even lead research in interesting new directions, so I am definitely not suggesting outright discarding them; it's just that they don't really deserve special consideration until they show themselves useful)

Currently, it is not incorrect to say that biological evolution is pinned to nucleic acids. Like all things scientific, such a statement is provisional and will be amended if evidence shows otherwise. This understanding should be implicit in any statements about science, and I read Hat Monster's (and everyone else's) statements with that implicit understanding.

I'm sorry to seem like a jerk, but I think you are objecting over something that is not really an issue.

Any claim otherwise is going to need at the very least a very solid model, and even better, experimental support of such a model.

I have no desire to claim otherwise, I just don't like a definition that cannot accomodate phenomena we have no direct experience with.

We should be able to encounter something new or find evidence of something old and be able to say "that's evolution" even if we have no prior knowledge of it. It seems very obvious to me that if we found life on Enceladus that didn't use nucleic acids, there would be no difficulty talking about it in evolutionary terms. That being the case, nucleic acids do not own the definition of evolution. So what does?

That being the case, nucleic acids do not own the definition of evolution. So what does?

Imperfect replicators would be my over-simplified answer.

Not so imperfect that there is no longevity in the information they replicate, but not so stable that there is no variation. Dawkins lays this idea out very well in the early chapters of "The Selfish Gene". If you haven't read it, then I highly recommend it. Like I said on the previous page in the thread, it opened my eyes to a lot of things I'd been confused about or had misunderstood about evolution.

Regarding finding life elsewhere, this is why I often add "on earth" when talking about the origin of life or origin of biological evolution. Since life on earth is the only life we know right now, such a qualifier should not be necessary, because statements about such things should be taken as provisional and based on current evidence. However, I've run into enough people thinking I'm trying to make claims about the entire universe with my statements (or at least try to twist my words that way) that I started adding it to pre-emptively avert that. This seems basically to be the issue that you are taking with Hat Monster's statements, no? Also, I like to try to think about evolution happening on different materials in other places as well. It's a fun thought experiment which appeals to the sci-fi buff, overly imaginative, curious child that I still am.

Even with that, I still think it's a stretch to call that the origin of biological evolution on Earth. I mean, you'd really have to show that such prion conformation evolution (remember, only conformations might be considered heredity, since there's no way to influence sequence replication) facilitated the origin of nucleic acid replication, and then those replicators took it from there under what we more easily recognize as biological evolution (more easily because of the clear mechanism of heredity). And, like I said, while the possibility, however small, does exist, I'd really prefer to see a good model and some good evidence to back it up.

My goal is not to make a case for the possibility, but rather object to that possibility being dismissed as an instance of evolution by natural selection as a matter of definition, even if it had happened.

Now it's been pointed out to me that "gene" does not strictly entail "nucleic acids", which was a point that hadn't occurred to me and could have caused confusion in the terminology I've used. In that sense proteins working the way I've described would in some sense be implementing genetic heritability.

But, Hat was specific in pinning evolution to nucleic acids, so my objection to that still stands.

If my idea can be dismissed by the science rather than by the definition, that would be entirely satisfactory for me. Its only purpose was to illustrate the gap I felt Hat's definition did not satisfactorily address.

That being the case, nucleic acids do not own the definition of evolution. So what does?

Imperfect replicators would be my over-simplified answer.

Differential reproductive success (for suitably loose definitions of "reproduction") probably needs to be in there too.

Nucleic acids are how it works on earth. If you want to study data on evolution, rather than fantasies, you need to be studying nucleic acids. Of course the definition can include other conceptual means of evolution, but they're all speculation without real-world data to study. Nucleic acid-based genetics is the only reality on which we can base the theory.

That being the case, nucleic acids do not own the definition of evolution. So what does?

Imperfect replicators would be my over-simplified answer.

Differential reproductive success (for suitably loose definitions of "reproduction") probably needs to be in there too.

Nucleic acids are how it works on earth. If you want to study data on evolution, rather than fantasies, you need to be studying nucleic acids. Of course the definition can include other conceptual means of evolution, but they're all speculation without real-world data to study. Nucleic acid-based genetics is the only reality on which we can base the theory.

That being the case, nucleic acids do not own the definition of evolution. So what does?

Imperfect replicators would be my over-simplified answer.

Differential reproductive success (for suitably loose definitions of "reproduction") probably needs to be in there too.

Nucleic acids are how it works on earth. If you want to study data on evolution, rather than fantasies, you need to be studying nucleic acids. Of course the definition can include other conceptual means of evolution, but they're all speculation without real-world data to study. Nucleic acid-based genetics is the only reality on which we can base the theory.

It can be valuable to explore fictional worlds created by simulations, but they are still fictional. If you can access real-world data, there are no ifs. Comparison of simulations to their predictions can be a useful technique.

That being the case, nucleic acids do not own the definition of evolution. So what does?

Imperfect replicators would be my over-simplified answer.

Differential reproductive success (for suitably loose definitions of "reproduction") probably needs to be in there too.

That would be natural selection. Evolution doesn't require natural selection, in theory, and may occur by random drift. But in that case there would be no "adaptation", only neutral evolution. Note that most genetic changes in natural populations seem to occur by drift, as they mostly involve synonymous mutations. That's still evolution.